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Resource:InnateDB

Name: Resource:InnateDB
Description: Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.

Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases.

InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions.

InnateDB Capabilities:

  • View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly.
  • Search for genes and proteins of interest.
  • Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc.
  • Search genes/interactions belonging to 3,900 pathways.
  • Visualize interactions using an intuitive subcellular localization-based layout in Cerebral.
  • Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more.
  • Access curated interaction data via a dedicated PSICQUIC webservice.
Other Name(s): InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways, InnateDB: Systems Biology of the Innate Immune Response
Abbreviation: InnateDB
Parent Organization: Simon Fraser University; British Columbia; Canada, University of British Columbia; British Columbia; Canada, Teagasc; Ireland
Supporting Agency: Genome Canada, Foundation for the National Institutes of Health, Teagasc, Canadian Institutes of Health Research, AllerGen
Grant: RMIS6018, 12ASI1, 12B&B2
Resource Type(s): Database, Data analysis service
Resource: Resource
URL: http://www.innatedb.com
*Id: nif-0000-20808
PMID: PMID 23180781, 18766178
Publication link: http://nar.oxfordjournals.org/content/41/D1/D1228.long
Related condition/disease: microbial infection, allergy, asthma
Related to: Resource:IMEx - The International Molecular Exchange Consortium, Resource:PSICQUIC, Resource:GO, Resource:re3data.org
Availability: Public, Acknowledgement requested, Curated interactions are licensed under the, Design Science License, All other data is licensed under the terms of the originating database.
Address: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
Keywords: gene, Immune response, pathway, protein, signaling pathway, interaction, immune, signaling response, gene, orthology prediction, orthology, Ortholg, annotation, interactome, gene expression, molecule, protein-protein interaction, molecular interaction, visualization, nucleic acid-protein, nucleic acid, Network, Web service, Transcription Factor Binding Site, Software resource
Organism: Human, Mouse, Bos taurus
Link to OWL / RDF: Download this content as OWL/RDF

Categories related to Resource:InnateDB

Resource:ConsensusPathDB, Resource:IMEx - The International Molecular Exchange Consortium, Resource:IntAct, Resource:Interaction Reference Index, Resource:PSICQUIC Registry

Curation status: Uncurated

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Notes

This page uses this default form:Resource

Alt. URL: http://www.innatedb.ca
Mirror URL (Ireland): http://innatedb.teagasc.ie/

Contributors

Aarnaud, Ccdbuser, Yazin



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*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.

Facts about Resource:InnateDBRDF feed
AbbrevInnateDB  +
AddressDepartment of Molecular Biology and Biochemistry  +, Simon Fraser University  +, Burnaby  +, British Columbia  +, and Canada  +
AvailabilityPublic  +, Acknowledgement requested  +, Curated interactions are licensed under the  +, Design Science License  +, and All other data is licensed under the terms of the originating database.  +
CommentType: Disciplinary
CurationStatuscurated  +
DefiningCitationhttp://www.innatedb.com  +
DefinitionPublicly available database of the genes, Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.

Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases.

InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions.

InnateDB Capabilities:

  • View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly.
  • Search for genes and proteins of interest.
  • Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc.
  • Search genes/interactions belonging to 3,900 pathways.
  • Visualize interactions using an intuitive subcellular localization-based layout in Cerebral.
  • Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more.
  • Access curated interaction data via a dedicated PSICQUIC webservice. data via a dedicated PSICQUIC webservice.
ExampleImageInnateDB.PNG  +
GrantCategory:RMIS6018   +, Category:12ASI1   +, and Category:12B&B2   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +, and Data analysis service  +
Idnif-0000-20808  +
Is part ofSimon Fraser University; British Columbia; Canada  +, University of British Columbia; British Columbia; Canada  +, and Teagasc; Ireland  +
KeywordsGene  +, Immune response  +, Pathway  +, Protein  +, Signaling pathway  +, Interaction  +, Immune  +, Signaling response  +, Orthology prediction  +, Orthology  +, Ortholg  +, Annotation  +, Interactome  +, Gene expression  +, Molecule  +, Protein-protein interaction  +, Molecular interaction  +, Visualization  +, Nucleic acid-protein  +, Nucleic acid  +, Network  +, Web service  +, Transcription Factor Binding Site  +, and Software resource  +
LabelResource:InnateDB  +
ModifiedDate16 June 2014  +
PMID23180781, 18766178  +
Page has default formThis property is a special property in this wiki.Resource  +
PublicationLinkhttp://nar.oxfordjournals.org/content/41/D1/D1228.long  +
RelatedToResource:IMEx - The International Molecular Exchange Consortium  +, Resource:PSICQUIC  +, Resource:GO  +, and Resource:re3data.org  +
Related diseaseMicrobial infection  +, Allergy  +, and Asthma  +
SpeciesHuman  +, Mouse  +, and Bos taurus  +
SuperCategoryResource  +
Supporting AgencyGenome Canada  +, Foundation for the National Institutes of Health  +, Teagasc  +, Canadian Institutes of Health Research  +, and AllerGen  +
SynonymInnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways  +, and InnateDB: Systems Biology of the Innate Immune Response  +